package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.validation.Valid;
import jakarta.validation.constraints.Max;
import jakarta.validation.constraints.Min;
import java.util.Collection;
import java.util.List;
import org.cbioportal.legacy.model.MolecularProfile;
import org.cbioportal.legacy.model.meta.BaseMeta;
import org.cbioportal.legacy.service.MolecularProfileService;
import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.legacy.service.exception.StudyNotFoundException;
import org.cbioportal.legacy.web.config.PublicApiTags;
import org.cbioportal.legacy.web.config.annotation.PublicApi;
import org.cbioportal.legacy.web.parameter.Direction;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.cbioportal.legacy.web.parameter.MolecularProfileFilter;
import org.cbioportal.legacy.web.parameter.PagingConstants;
import org.cbioportal.legacy.web.parameter.Projection;
import org.cbioportal.legacy.web.parameter.sort.MolecularProfileSortBy;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

@PublicApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = PublicApiTags.MOLECULAR_PROFILES, description = " ")
public class MolecularProfileController {

  @Autowired private MolecularProfileService molecularProfileService;

  @RequestMapping(
      value = "/molecular-profiles",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get all molecular profiles")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(array = @ArraySchema(schema = @Schema(implementation = MolecularProfile.class))))
  public ResponseEntity<List<MolecularProfile>> getAllMolecularProfiles(
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection,
      @Parameter(description = "Page size of the result list")
          @Max(PagingConstants.MAX_PAGE_SIZE)
          @Min(PagingConstants.MIN_PAGE_SIZE)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
          Integer pageSize,
      @Parameter(description = "Page number of the result list")
          @Min(PagingConstants.MIN_PAGE_NUMBER)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
          Integer pageNumber,
      @Parameter(description = "Name of the property that the result list is sorted by")
          @RequestParam(required = false)
          MolecularProfileSortBy sortBy,
      @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
          Direction direction) {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          molecularProfileService.getMetaMolecularProfiles().getTotalCount().toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          molecularProfileService.getAllMolecularProfiles(
              projection.name(),
              pageSize,
              pageNumber,
              sortBy == null ? null : sortBy.getOriginalValue(),
              direction.name()),
          HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/molecular-profiles/{molecularProfileId}",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get molecular profile")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content = @Content(schema = @Schema(implementation = MolecularProfile.class)))
  public ResponseEntity<MolecularProfile> getMolecularProfile(
      @Parameter(required = true, description = "Molecular Profile ID e.g. acc_tcga_mutations")
          @PathVariable
          String molecularProfileId)
      throws MolecularProfileNotFoundException {

    return new ResponseEntity<>(
        molecularProfileService.getMolecularProfile(molecularProfileId), HttpStatus.OK);
  }

  @PreAuthorize(
      "hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/studies/{studyId}/molecular-profiles",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get all molecular profiles in a study")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(array = @ArraySchema(schema = @Schema(implementation = MolecularProfile.class))))
  public ResponseEntity<List<MolecularProfile>> getAllMolecularProfilesInStudy(
      @Parameter(required = true, description = "Study ID e.g. acc_tcga") @PathVariable
          String studyId,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection,
      @Parameter(description = "Page size of the result list")
          @Max(PagingConstants.MAX_PAGE_SIZE)
          @Min(PagingConstants.MIN_PAGE_SIZE)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
          Integer pageSize,
      @Parameter(description = "Page number of the result list")
          @Min(PagingConstants.MIN_PAGE_NUMBER)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
          Integer pageNumber,
      @Parameter(description = "Name of the property that the result list is sorted by")
          @RequestParam(required = false)
          MolecularProfileSortBy sortBy,
      @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
          Direction direction)
      throws StudyNotFoundException {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          molecularProfileService
              .getMetaMolecularProfilesInStudy(studyId)
              .getTotalCount()
              .toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          molecularProfileService.getAllMolecularProfilesInStudy(
              studyId,
              projection.name(),
              pageSize,
              pageNumber,
              sortBy == null ? null : sortBy.getOriginalValue(),
              direction.name()),
          HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/molecular-profiles/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Fetch molecular profiles")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(array = @ArraySchema(schema = @Schema(implementation = MolecularProfile.class))))
  public ResponseEntity<List<MolecularProfile>> fetchMolecularProfiles(
      @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
          @RequestAttribute(required = false, value = "involvedCancerStudies")
          Collection<String> involvedCancerStudies,
      @Parameter(
              hidden =
                  true) // prevent reference to this attribute in the swagger-ui interface. this
          // attribute is needed for the @PreAuthorize tag above.
          @Valid
          @RequestAttribute(required = false, value = "interceptedMolecularProfileFilter")
          MolecularProfileFilter interceptedMolecularProfileFilter,
      @Parameter(
              required = true,
              description = "List of Molecular Profile IDs or List of Study IDs")
          @Valid
          @RequestBody(required = false)
          MolecularProfileFilter molecularProfileFilter,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection) {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      BaseMeta baseMeta;

      if (interceptedMolecularProfileFilter.getStudyIds() != null) {
        baseMeta =
            molecularProfileService.getMetaMolecularProfilesInStudies(
                interceptedMolecularProfileFilter.getStudyIds());
      } else {
        baseMeta =
            molecularProfileService.getMetaMolecularProfiles(
                interceptedMolecularProfileFilter.getMolecularProfileIds());
      }
      responseHeaders.add(HeaderKeyConstants.TOTAL_COUNT, baseMeta.getTotalCount().toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      List<MolecularProfile> molecularProfiles;
      if (interceptedMolecularProfileFilter.getStudyIds() != null) {
        molecularProfiles =
            molecularProfileService.getMolecularProfilesInStudies(
                interceptedMolecularProfileFilter.getStudyIds(), projection.name());
      } else {
        molecularProfiles =
            molecularProfileService.getMolecularProfiles(
                interceptedMolecularProfileFilter.getMolecularProfileIds(), projection.name());
      }
      return new ResponseEntity<>(molecularProfiles, HttpStatus.OK);
    }
  }
}
